News & Highlights

Contents

We have a new Doctor in the house (Dr. Chuan Tian)


Congratulations to Dr. Chuan Tian on successfully defending his thesis on 21 November 2019. Under the guidance of Prof. Carlos Simmerling, Chuan designed the new Amber protein forcefield ff19SB. ff19SB has significantly improved the backbone profiles for all 20 amino acids. His extremely good-natured personality along with his attention to detail, intellectual abilities, strong work ethics, and unwillingness to quit are some of the reasons the project has been successful.

Check out the ff19SB Paper: https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00591



Koushik at Molecular Biophysics in the Northeast Meeting


Koushik was one of the selected speakers at the Molecular Biophysics in the Northeast Meeting which was held at Northeastern University in Boston. This meeting was the first one and provided an opportunity for members of the experimental and theoretical molecular biophysics community to discuss current research topics. https://web.northeastern.edu/biophyssymposium/

He presented on the technique and applications of reservoir REMD. Look out for his publication coming soon. While in Boston he also met with some exemplary past members of the Lab (James Maier and He Huang).


Chemistry Research Day


Chemistry Research day is an opportunity for students to showcase their hard work in the form of poster presentations. The Simmerling Lab showed up in droves, exhibiting an array of computational methodologies and applications. Most importantly, our young scientists (undergraduates Jose, Jorge, Kelly, and Abby) got the opportunity to present and share their research with the University Community. We are so proud of them!



We have a new Doctor in the house (Dr. Junjie Zou)


Congratulations to Dr. Junjie Zou on successfully defending his thesis. Junjie was a joint student in our lab and Raleigh's Lab. He mastered the art of doing both computational and experimental research simultaneously while completing his Ph.D. Junjie performed groundbreaking work on the use of Thermodynamic Integration for Free energy calculations to study mutational effects and drug binding.

New publication on winning 2018 D3R Grand Challenge 4

In the framework of the 2018 Drug Design Data Resource (D3R) grand challenge 4, blinded predictions on relative binding free energy were performed for a set of 39 ligands of the Cathepsin S. We leveraged the GPU-accelerated thermodynamic integration (GTI) of Amber 18 to advance our computational prediction. We outperformed all other participants in this session. The success in a blinded prediction strongly suggests that alchemical free energy calculation in Amber is a promising tool for future commercial drug design.

https://doi.org/10.26434/chemrxiv.8312375.v1

New publication (preprint) on our new protein force field ff19SB

After several years of work, we are excited to announce our new protein force field ff19SB. Our lab’s prior protein force fields are the most commonly used models in Amber, and are also widely implemented in other programs. Our ff99SB model has been cited nearly 5,000 times. Our follow up ff14SB has been cited nearly 1,500 times. Despite this wide use, we show that the protein backbone treatment in these force fields is the limiting factor in accuracy for many simulations, and the models are unable to reproduce differences in key properties such as changes to backbone conformational preferences among different amino acids. In the updated model ff19SB, we have significantly improved the backbone profiles for all 20 amino acids. We hope that our new ff19SB model will see wide use and have a favorable impact in the community.

https://doi.org/10.26434/chemrxiv.8279681.v1

Congratulations to Seungyoun on Defending her Masters Thesis

Seungyoun Shin completed another chapter in her quest to become a Scientist. She defended her Masters thesis with the recommendation from her committee to join the Ph.D. Program at SBU.


Simmerling's Lab at MACC-NYGAIM


Members of the Simmerling's Lab traveled to NYC to present posters on their research in the Lab. They got the opportunity to interact and network with some of the leading scientists in both the Pharmaceutical Industry and Academia. While at MACC, they met a former graduate student, now Professor at BMCC (Lauren Wickstrom)


IACS Research Day


Kellon and Lauren gave a 2 minute presentation (lightning talk), and a poster presentation at IACS research day on their research.


Chuan Tian's first ACS Oral Presentation on ff19SB


Giving an oral presentation at a national meeting such as the ACS is an outstanding accomplishment. It is a demonstration of the hard work Chuan put in on the development of ff19SB. Chuan at 2019 ACS Orlando

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Simmerling's Lab at the Amber Meeting


Every year the Amber developers meet to discuss new ideas and methods to implement into Amber.

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New Student Yuzhang Wang


Welcome Yuzhang Wang to the Simmerling lab! Yuzhang is joining us from Beihang University in China.

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IACS Travel Scholarship awarded to Chuan Tian

Congratulations to Chuan Tian on being awarded an IACS Travel Scholarship. Chuan will use this travel award to give an oral presentation at the spring 2019 National ACS meeting in April.

https://iacs.stonybrook.edu/_archived/awards/travel.html

New publication alert from Dr. He (Agnes) Huang

Congratulations to Agnes on her first-author JCTC article! While in the Simmerling Lab, Agnes worked on a faster implementation of calculating the Solvent Accessible Surface Area for biomolecules simulated in an implicit solvent. She leveraged the numerous cores on the GPU to increase the speed of her algorithm. Check out Agnes new paper below and look out for this new code in Amber19. Soon you can be estimating the non-polar contribution in your simulations without a noticeable slow down in your implicit solvent calculations.

https://pubs.acs.org/doi/full/10.1021/acs.jctc.8b00413

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Simmerling Lab at the BNL GPU Hackathon


Members of the Simmerling Lab took part in a week-long GPU Hackathon hosted by Brookhaven National Lab from 17th to the 21st of September. https://www.bnl.gov/newsroom/news.php?a=213093 The team consisted of Zach Fallon, Lauren Raugette, Kellon Belfon, and Chuan Tian. The goal of the team was to port the Center of Mass (CoM) Angle and Dihedral code into Amber18 PMEMD and PMEMD.cuda. Dr. Kevin Hauser, a past student in the lab was also instrumental in the team success by writing the CUDA kernels necessary for the CoM calculations. The team was successful in getting the CoM code working with the help of the mentors at the hackathon, Dr. Daniel Tian (NVIDIA) and Dr. Li Tang (BNL).


Chuan Tian at the 256th ACS National Meeting


One of the most rewarding parts of research is presenting your work to other scientists. Chuan Tian got the opportunity to present a poster at the 256th ACS National Meeting in Boston. The title of his poster was "FF18SB: Improving the accuracy of Biomolecular Simulations". Look out for more information on this new forcefield. Outstanding work Chuan!

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Congratulations Dr. Angela Migues!


Dr. Angela Migues, a post-doc in our lab received a new position at SUNY Oneonta. She was helpful with the forcefield project and her research involved understanding replication fidelity in DNA Polymerase. All the best in your new position, we know you will do an excellent job.

Angela last words to the lab:

"Don't be afraid to make mistakes, I have learned far more from my failures than my success"


2018 Sigma Xi Travel Award


Congratulations to Chuan Tian on your Sigma Xi Travel Award (2018). https://www.sigmaxi.org/programs/grants-in-aid

We have a new Doctor in the house (Dr Huang He)


Congratulations to Dr. Huang He 黄鹤 (Agnes) on successfully defending her thesis. During her Ph.D., Agnes created a faster method to calculate the non-polar solvation energy for MD simulation. She achieved this by leveraging the parallel architecture of GPUs. Look out for Agnes new code in Amber 18.


Lauren Raguette awarded the best Teaching Assistant by Chemistry department


Congratulations Lauren on your Chemistry Award for First-Year Graduate Student Teaching Assistant. It is an honor to be awarded for your ability to make a tangible change in the education of the Undergraduates in the Chemistry department.

Ruth L. Kirschstein Predoctoral Individual National Research Service Award to Kellon Belfon


Kellon's NRSA F31 application was selected for funding by the National Institute of General Medical Sciences. This award provides predoctoral individuals with supervised research training in specified health and health-related areas leading toward the research doctoral degree.

New Student Seungyoun Shin


Welcome, Seungyoun Shin to the Simmerling lab! Seungyoun is joining us from St. Edward's University.

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New Student Lauren Raguette


Welcome Lauren Raguette to the Simmerling lab! Lauren is joining us from Villanova University.

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ACM-SIGHPC/Intel Data Science Fellowship Award to Kellon Belfon


Congratulations to Kellon Belfon for winning the prestigious Association of Computing Machinery (ACM) Special Interest Group on High-Performance Computing (SIGHPC)/Intel Computational Science and Data Science Fellowship! http://www.sighpc.org/fellowships/2017

Kellon is one of only 12 recipients for this award worldwide. Awardees were chosen based on their overall potential for excellence in data science and/or computational science, and the extent to which they will serve as leaders and role models to increase diversity in the workplace.

He was featured in SBU happening below http://www.stonybrook.edu/happenings/featuredpost/kellon-belfon-finds-his-way-from-grenada-to-prestigious-fellowship/

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Regeneron Science Talent Search


Annie Chang, a high school student from the Simmerling lab, was selected as one of the top 300 scholars in the prestigious national Regeneron Science Talent Search. Annie's project involved understanding the different effects that strong and weak inhibitors have on the dynamics of HIV protease's flaps. For her achievement, she was awarded $2000, a one-year subscription to Science News, and a certificate. Congratulations Annie

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https://student.societyforscience.org/regeneronsts-scholars-2017

2016 7th Annual CFN Image Challenge Winner (Chuan Tian)


Congratulation Chuan Tian on being the winner of Brookhaven National Lab CFN image competition.

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Here is the announcement http://simmerlinglab.org/wiki/images/8/80/7th_Annual_CFN_Image_Challenge_Winner%2C_CFN_Retreat_in_BNL.pdf

New Student Zachary Fallon


Welcome, Zachary Fallon to the Simmerling lab! Zach is joining us from Adelphi University.

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New publication alert from Haoquan Li

"Congratulations to Haoquan for his first-author JACS article! Even though he has gone on to other things since being in our group, he did a really impressive job of continuing to move this project forward and finish another really strong paper." - Prof. Simmerling

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"Here, we use molecular dynamics simulations to explore the mechanism by which OGG1 discriminates between 8-oxoG and guanine along the base eversion pathway. MD results suggest an important role for kinking of the DNA by the glycosylase, which positions DNA phosphates in a way that assists lesion recognition during base eversion. The computational predictions were validated through experimental enzyme assays on phosphorothioate substrate analogs. Our simulations suggest that OGG1 distinguishes between 8-oxoG and G using their chemical dissimilarities not only at the active site, but also at earlier stages during base eversion, and this mechanism is at least partially conserved in Fpg despite lack of structural homology. The similarity also suggests that lesion recognition through multiple gating steps may be a common theme in DNA repair. Our results provide new insight into how enzymes can exploit kinetics and DNA conformational changes to probe the chemical modifications present in DNA lesions." - excerpt from the Abstract.

Check out the paper below

DNA deformation-coupled recognition of 8-oxoguanine: conformational kinetic gating in human DNA glycosylase.
Li, Haoquan; Endutkin, Anton; Bergonzo, Christina; Lin, Fu; Grollman, Arthur P.; Zharkov, Dmitry O.; Simmerling, Carlos, Journal of the American Chemical Society, 2016 accepted

A new doctor in the house [Kevin Hauser]


Dr. Kevin Hauser defended his thesis with an exciting talk that shed light on how a transcription factor, MTERF, search and recognize a specific sequence on DNA. His research focused on developing a model of protein-DNA search and recognition which described a sliding mechanism of MTERF on DNA.


Siemens Science competition semi-finalists


The Siemens Science Competition semi-finalists list is out [1] and Annie Chang is on it. Annie is a high school student that participated in the Siemens Science Research Program at SBU, this summer. She performed research in the Simmerling lab on understanding the effect of various drugs on HIV-1 PR flap dynamics. Congratulations on making it to the semi-finals.

New publication from Junjie Zou


Junjie Zou, a graduate student in the Simmerling and Raleigh lab, published his first paper in the lab. Outstanding job Junjie, congratulations!

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Experimental and Computational Analysis of Protein Stabilization by Gly-to-D-Ala Substitution: A Convolution of Native State and Unfolded State Effects
Zou, Junjie; Song, Benben; Simmerling, Carlos; Raleigh, Daniel, Journal of the American Chemical Society, 2016 accepted

Congratulations Kevin Hauser!


Kevin Hauser started a post-doctoral position at Schrödinger. All the best Kevin, we know you will shine in your new position.

Congratulations Professor Simmerling!


Professor Carlos Simmerling was selected to the 2016 class of ACS Fellows, an elite group of 57 distinguished scientists who have made outstanding achievements in chemistry and contributed to the profession, science and ACS organization. Professor Simmerling was recognized at a ceremony on August 22, during the 252nd National ACS Meeting and Exposition in Philadelphia.

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Check out Professor Simmerling and the other 57 members of the 2016 class of ACS fellows:

https://www.acs.org/content/acs/en/funding-and-awards/fellows.html

Congratulations to Gabriela and Victoria!


Victoria and Gabriela (Undergraduates in the Simmerling lab) got accepted into the Ph.D. program at the University of Florida and the University of Pennsylvania respectively. All the best ladies in your future endeavors.

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Recently Published Manuscripts

Blinded Prediction of Protein-Ligand Binding Affinity Using Amber Thermodynamic Integration for the 2018 D3R Grand Challenge 4
Junjie Zou, Chuan Tian, Carlos Simmerling, ChemRxiv. Preprint, 2019,
DOI:10.26434/chemrxiv.8312375.v1

A Fast Implementation of the Nudged Elastic Band Method in AMBER
Delaram Ghoreishi, David Cerutti, Zachary Fallon, Carlos Simmerling, Adrian Roitberg, ChemRxiv. Preprint, 2019,
DOI: 10.26434/chemrxiv.8283554.v1

ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution
Chuan Tian, Koushik Kasavajhala, Kellon Belfon, Lauren Raguette, He Huang, Angela Migues, John Bickel, Yuzhang Wang, Jorge Pincay, Qin Wu, Carlos Simmerling, ChemRxiv. Preprint, 2019,
DOI: 10.26434/chemrxiv.8279681.v1

Base flipping by MTERF1 can accommodate multiple conformations and occurs in a stepwise fashion
Byrnes, J.; Hauser, K.; Mejia, E.,; Norona, L.; Simmerling, C.; Garcia-Diaz, M.,J. Mol. Biol., 2016, 428 (12), 2542–2556


Advances in free-energy-based simulations of protein folding and ligand binding
Perez, A., Morrone, J. A., Simmerling, C., Dill, A.,Current opinion in structural biology 2016, 36, 25–31

A Dynamic Checkpoint in Oxidative Lesion Discrimination by Formamidopyrimidine–DNA Glycosylase
Li, H., Endutkin, A., Bergonzo, C., Grollman, A.; Campbell, A., de los Santos, C., Zharkov, D., Simmerling, C.,Nucleic Acids Research, 44 (2), 683–694

A human transcription factor in search mode
Hauser, K.; Essuman, B.; He, Y.; Coutsias, E.; Garcia-Diaz, M.; Simmerling, C., Nucleic Acids Research, 44 (1), 63–74

A grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations
Perez, A., MacCallum, JL., Brini, E., Simmerling, C., Dill, KA, J. Chem. Theor. Comput., 2015, 11 (10), 4770–4779
DOI: 10.1021/acs.jctc.5b00662



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